Replace `prefix` with `pathvars`

[irm-codebase]

Is your feature request related to a problem? Please describe.
Using prefixes in the modules often leads to the need to 'copy paste' files around, or to re-wire rules using the with: statement.

A recent snakemake update added pathvars, which could be used as a cleaner input/output specification for the module
https://snakemake.readthedocs.io/en/stable/snakefiles/modularization.html#pathvars

We should look into these, and perhaps replace prefix in the integration test and add examples into the template itself.

[irm-codebase]

Note: if this is done, we must also update snakefmt to the newest version in the pre-commit-ci configuration